Molecular marker mapping of leaf rust resistance gene lr46 and its association with stripe rust resistance gene yr29 in wheat

Genetic mapping and marker development for resistance of wheat against the root lesion nematode Pratylenchus neglectus

BACKGROUND

The Rlnn1 locus, which resides on chromosome 7A of bread wheat (Triticum aestivum L.) confers moderate resistance against the root lesion nematode Pratylenchus neglectus. Prior to this research, the exact linkage relationships of Rlnn1 with other loci on chromosome 7A were not clear and there were no simple codominant markers available for selection of Rlnn1 in wheat breeding. The objectives of the research reported here were to (1) develop an improved genetic map of the Rlnn1 region of chromosome 7A and (2) develop molecular markers that could be used in marker-assisted selection to improve resistance of wheat against P. neglectus.

RESULTS

A large-effect quantitative trait locus (QTL) for resistance against P. neglectus was genetically mapped using a population of Excalibur/Kukri doubled haploid lines. This QTL coincides in position with the rust resistance gene(s) Lr20/Sr15, the phytoene synthase gene Psy-A1 and 10 molecular markers, including five new markers designed using wheat-rice comparative genomics and wheat expressed sequence tags. Two of the new markers are suitable for use as molecular diagnostic tools to distinguish plants that carry Rlnn1 and Lr20/Sr15 from those that do not carry these resistance genes.

CONCLUSIONS

The genomic location of Rlnn1 was confirmed to be in the terminal region of the long arm of chromosome 7A. Molecular markers were developed that provide simple alternatives to costly phenotypic assessment of resistance against P. neglectus in wheat breeding. In Excalibur, genetic recombination seems to be completely suppressed in the Rlnn1 region.

Fine mapping quantitative resistances to downy mildew in lettuce revealed multiple sub-QTLs with plant stage dependent effects reducing or even promoting the infection

KEY MESSAGE

Three regions with quantitative resistance to downy mildew of non-host and wild lettuce species, Lactuca saligna , disintegrate into seventeen sub-QTLs with plant-stage-dependent effects, reducing or even promoting the infection. Previous studies on the genetic dissection of the complete resistance of wild lettuce, Lactuca saligna, to downy mildew revealed 15 introgression regions that conferred plant stage dependent quantitative resistances (QTLs). Three backcross inbred lines (BILs), carrying an individual 30-50 cM long introgression segment from L. saligna in a cultivated lettuce, L. sativa, background, reduced infection by 60-70 % at young plant stage and by 30-50 % at adult plant stage in field situations. We studied these three quantitative resistances in order to narrow down their mapping interval and determine their number of loci, either single or multiple. We performed recombinant screenings and developed near isogenic lines (NILs) with smaller overlapping L. saligna introgressions (substitution mapping). In segregating introgression line populations, recombination was suppressed up to 17-fold compared to the original L. saligna × L. sativa F 2 population. Recombination suppression depended on the chromosome region and was stronger suppressed at the smallest introgression lengths. Disease evaluation of the NILs revealed that the resistance of all three BILs was not explained by a single locus but by multiple sub-QTLs. The 17 L. saligna-derived sub-QTLs had a smaller and plant stage dependent resistance effect, some segments reducing; others even promoting downy mildew infection. Implications for lettuce breeding are outlined.

Genetic Analysis of Adult Plant Resistance to Yellow Rust and Leaf Rust in Common Spring Wheat Quaiu 3

Identifying and utilizing rust resistance genes in wheat has been hampered by the continuous and rapid emergence of new pathogen races. A major focus of many wheat breeding programs is achieving durable adult plant resistance (APR) to yellow (stripe) rust (YR) and leaf (brown) rust (LR), caused by Puccinia striiformis and P. triticina, respectively. This study aimed to determine the genetic basis of resistance to YR and LR in the common spring wheat 'Quaiu 3'. To that end, we evaluated 198 F₅ recombinant inbred lines (RILs), derived from a cross of susceptible 'Avocet-YrA' with Quaiu 3, for APR to LR and YR in artificially inoculated field trials conducted in Mexico during the 2009 and 2010 growing seasons. High narrow-sense heritability (h²) estimates, ranging between 0.91 and 0.95, were obtained for both LR and YR disease severities for both years. The quantitative and qualitative approaches used to estimate gene numbers showed that, in addition to known resistance genes, there are at least two to three APR genes associated with LR and YR resistance in the RIL population. The moderately effective race-specific resistance gene Lr42 and the pleiotropic slow-rusting APR gene Lr46/Yr29 were found to interact with additional unidentified APR genes. The unidentified APR genes should be of particular interest for further characterization through molecular mapping, and for utilization by wheat breeding programs.

Histological and cytological characterization of adult plant resistance to wheat stripe rust

Wheat cultivar Xingzi 9104 (XZ) possesses adult plant resistance (APR) to stripe rust caused by Puccinia striiformis f. sp. tritici (Pst). In this study, histological and cytological experiments were conducted to elucidate the mechanisms of APR in XZ. The results of leaf inoculation experiments indicated that APR was initiated at the tillering stage, gradually increased as the plant aged and highly expressed after boot stage. The histology and oxidative burst in infected leaves of plants at seedling, tillering and boot stages were examined using light microscopic and histochemical methods. Subcellular changes in the host-pathogen interactions during the seedling and boot stages were analyzed by transmission electron microscopy. The results showed that haustorium formation was retarded in the adult plants and that the differentiation of secondary intercellular hyphae was significantly inhibited, which decreased the development of microcolonies in the adult plants, especially in plants of boot stage. The expression of APR to stipe rust during wheat development was clearly associated with extensive hypersensitive cell death of host cells and localized production of reactive oxygen species, which coincided with the restriction of fungal growth in infection sites in adult plants. At the same time, cell wall-related resistance in adult plants prevented ingression of haustorial mother cells into plant cells. Haustorium encasement was coincident with malformation or death of haustoria. The results provide useful information for further determination of mechanisms of wheat APR to stripe rust.

KEY MESSAGE

The expression of APR to stipe rust in wheat cultivar Xingzi 9104 (XZ) was clearly associated with extensive hypersensitive cell death of host cells and the localized production of reactive oxygen species.

QTL mapping of adult-plant resistances to stripe rust and leaf rust in Chinese wheat cultivar Bainong 64

Stripe rust and leaf rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. and P. triticina, respectively, are devastating fungal diseases of common wheat (Triticum aestivum L.). Chinese wheat cultivar Bainong 64 has maintained acceptable adult-plant resistance (APR) to stripe rust, leaf rust and powdery mildew for more than 10 years. The aim of this study was to identify quantitative trait loci/locus (QTL) for resistance to the two rusts in a population of 179 doubled haploid (DH) lines derived from Bainong 64 × Jingshuang 16. The DH lines were planted in randomized complete blocks with three replicates at four locations. Stripe rust tests were conducted using a mixture of currently prevalent P. striiformis races, and leaf rust tests were performed with P. triticina race THTT. Leaf rust severities were scored two or three times, whereas maximum disease severities (MDS) were recorded for stripe rust. Using bulked segregant analysis (BSA) and simple sequence repeat (SSR) markers, five independent loci for APR to two rusts were detected. The QTL on chromosomes 1BL and 6BS contributed by Bainong 64 conferred resistance to both diseases. The loci identified on chromosomes 7AS and 4DL had minor effects on stripe rust response, whereas another locus, close to the centromere on chromosome 6BS, had a significant effect only on leaf rust response. The loci located on chromosomes 1BL and 4DL also had significant effects on powdery mildew response. These were located at the same positions as the Yr29/Lr46 and Yr46/Lr67 genes, respectively. The multiple disease resistance locus for APR on chromosome 6BS appears to be new. All three genes and their closely linked molecular markers could be used in breeding wheat cultivars with durable resistance to multiple diseases.

Molecular mapping of stripe rust resistance gene YrSN104 in Chinese wheat line Shaannong 104

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a serious yield-limiting factor for wheat production worldwide. The objective of this study was to identify and map a stripe rust resistance gene in wheat line Shaannong 104 using SSR markers. F(1), F(2) and F(3) populations from Shaannong 104/Mingxian 169 were inoculated with Chinese Pst race CYR32 in a greenhouse. Shaannong 104 carried a single dominant gene, YrSN104. Six potential polymorphic SSR markers identified in bulk segregant analysis were used to genotype F(2) and F(3) families. YrSN104 was closely linked with all six SSR markers on chromosome 1BS with genetic distances of 2.0 cM (Xgwm18, Xgwm273, Xbarc187), 2.6 cM (Xgwm11, Xbarc137) and 5.9 cM (Xbarc240). Pedigree analysis, pathogenicity tests using 26 Pst races, haplotyping of associated markers on isogenic lines carrying known stripe rust resistance genes, and associations with markers suggested that YrSN104 was a new resistance gene or an allele at the Yr24/Yr26 locus on chromosome 1BS. Deployment of YrSN104 singly or in combination to elite genotypes could play an effective role to lessen yield losses caused by stripe rust.

Partial resistance to powdery mildew in German spring wheat 'Naxos' is based on multiple genes with stable effects in diverse environments

Powdery mildew is one of the most important wheat diseases in temperate regions of the world. Resistance breeding is considered to be an economical and environmentally benign way to control this disease. The German spring wheat cv. 'Naxos' exhibits high levels of partial and race non-specific resistance to powdery mildew in the field and is a valuable source in resistance breeding. The main objective of the present study was to map the genetic factors behind the resistance in Naxos, based on a population of recombinant inbred lines (RIL) from a cross with the susceptible CIMMYT breeding line SHA3/CBRD. Powdery mildew severity was evaluated in six field trials in Norway and four field trials in China. The major quantitative trait locus (QTL) with resistance from Naxos was detected close to the Pm3 locus on 1AS in all environments, and explained up to 35% of the phenotypic variation. Naxos was shown to carry another major QTL on 2DL and minor ones on 2BL and 7DS. QTL with resistance from SHA3/CBRD were detected on 1RS, 2DLc, 6BL and 7AL. The QTL on the 1B/1R translocation showed highly variable effects across environments corresponding to known virulence differences against Pm8. SHA3/CBRD was shown to possess the Pm3 haplotype on 1AS, but none of the known Pm3a-g alleles. The RIL population did not provide any evidence to suggest that the Pm3 allele of SHA3/CBRD acted as a suppressor of Pm8.

Characterization of Resistance to Stripe Rust in Contemporary Cultivars and Lines of Winter Wheat from the Eastern United States

Stripe rust, caused by Puccinia striiformis f. sp. tritici, has been an important disease of winter wheat (Triticum aestivum) in the eastern United States since 2000, when a new strain of the pathogen emerged. The new strain overcame the widely used resistance gene, Yr9, and was more aggressive and better adapted to warmer temperatures than the old strain. Host resistance is the most effective approach to manage stripe rust. Winter wheat lines with resistance to the new strain in the field are common, but the genes conferring this resistance are mostly unknown. The objectives of this research were to characterize the all-stage resistance and adult-plant resistance (APR) to stripe rust in a representative group of contemporary winter wheat cultivars and breeding lines and to identify the resistance genes when possible. Of the 50 lines evaluated for all-stage resistance at the seedling stage, nearly all were susceptible to the new strain. Based on a linked molecular marker, seven lines had resistance gene Yr17 that confers resistance to both old and new strains; however, this resistance was difficult to identify in the seedling stage. Of the 19 lines evaluated for APR, all expressed APR compared with a very susceptible check. Nine had race-specific APR to the new strain and nine had APR to both old and new strains. The remaining line, 26R61, had all-stage resistance to the old strain (conferred by resistance gene Yr9) and a high level of APR to the new strain. APR was expressed as low infection type, low percent leaf area diseased, and long latent period at heading stage under both low and high temperature regimes and could be identified as early as jointing stage. Based on tests for linked molecular markers, the most widely used slow-rusting APR genes, Yr18 and Yr29, were not present in any of the lines. The results of this research indicate that effective all-stage resistance was conferred only by Yr17 and that APR was common and likely conferred by unknown race-specific genes rather than genes conferring slow rusting that are more likely to be durable.

[Genetic analysis and molecular mapping of stripe rust resistance gene in a restore line of Thermo-Photo sensitive hybrid wheat MR168]

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important limiting factor to popularize hybrid wheat. The objectives of this study were to map a stripe rust resistance gene in a Chinese thermo-photo-sensitive hybrid wheat restore line MR168 using gene postulation and SSR markers. MR168 was highly resistant to 23 Pst races including CYR29, CYR31, CYR32, and CYR33. The populations F1, BC1, F2, and F3 from the cross between MR168 and SY95-71 (a wheat cultivar susceptible to Pst races) were inoculated with the race of Pst CYR32 of China in greenhouse. MR168 carried a single dominant gene for resistance to CYR32, tentatively designated YrMR168. It originated from Liaochun 10, a spring wheat variety. A total of 183 F2 plants, the resistant and susceptible parents and resistant and susceptible bulks were used for resistance gene mapping with 329 pairs of wheat SSR markers.Five SSR markers on chromosome 1BS including Xgwm18, Xbarc187, Xwmc269, Xgwm273, and Xwmc406 were linked with YrMR168. The resistance gene was closely linked to Xgwm18 and Xbarc187 with the genetic distances of 1.9 and 2.4 cM, respectively. Xgwm18 and Xbarc187 could be used for molecular marker assisted selection of YrMR168 in hybrid wheat breeding program.

The genetic characterisation of stripe rust resistance in the German wheat cultivar Alcedo

Stripe rust resistance in the German winter wheat cv. Alcedo has been described as durable, the resistance having remained effective when grown extensively in Germany and Eastern Europe between 1975 and 1989. Genetic characterisation of field resistance in a cross between Alcedo and the stripe rust susceptible UK winter wheat cv. Brigadier identified two major QTL in Alcedo located on the long arms of chromosomes 2D (QPst.jic-2D) and 4B (QPst.jic-4B). Stripe rust resistance was evaluated by measuring the extent of fungal growth, percentage infection (Pi) and the necrotic/chlorotic response of the plant to infection, infection type (IT). Both QPst.jic-2D and QPst.jic-4B contributed significantly to the reduction in stripe rust infection (Pi), with QPst.jic-2D explaining up to 36.20% and QPst.jic-4B 28.90% of the phenotypic variation measured for Pi. Both QTL were identified by the IT phenotypic scores, with QPst.jic-2D in particular being associated with a strong necrotic phenotype (low IT), QPst.jic-2D explaining up to 53.10% of IT phenotypic variation and QPst.jic-4B 22.30%. In addition, two small effect QTL for field stripe rust resistance were identified in Brigadier, QPst.jic-1B on the long arm of chromosome 1B and QPst.jic-5A on the short arm of chromosome 5A. The influence of QPst.jic-1B was primarily seen with the Pi phenotype, contributing up to 13.10% of the explained phenotypic variation. QPst.jic-5A was only detected using an approximate multiple-QTL model and selecting markers linked to the major effect QTL, QPst.jic-2D and QPst.jic-4B as co-factors. Seedling stripe rust resistance was also mapped in the cross, which confirmed the location of Yr17 from Brigadier to the short arm of chromosome 2A. A seedling expressed QTL was also located in Alcedo that mapped to the same location as the field stripe rust resistance QPst.jic-2D.

An introgression on wheat chromosome 4DL in RL6077 (Thatcher*6/PI 250413) confers adult plant resistance to stripe rust and leaf rust (Lr67)

Adult plant resistance (APR) to leaf rust and stripe rust derived from the wheat (Triticum aestivum L.) line PI250413 was previously identified in RL6077 (=Thatcher*6/PI250413). The leaf rust resistance gene in RL6077 is phenotypically similar to Lr34 which is located on chromosome 7D. It was previously hypothesized that the gene in RL6077 could be Lr34 translocated to another chromosome. Hybrids between RL6077 and Thatcher and between RL6077 and 7DS and 7DL ditelocentric stocks were examined for first meiotic metaphase pairing. RL6077 formed chain quadrivalents and trivalents relative to Thatcher and Chinese Spring; however both 7D telocentrics paired only as heteromorphic bivalents and never with the multivalents. Thus, chromosome 7D is not involved in any translocation carried by RL6077. A genome-wide scan of SSR markers detected an introgression from chromosome 4D of PI250413 transferred to RL6077 through five cycles of backcrossing to Thatcher. Haplotype analysis of lines from crosses of Thatcher × RL6077 and RL6058 (Thatcher*6/PI58548) × RL6077 showed highly significant associations between introgressed markers (including SSR marker cfd71) and leaf rust resistance. In a separate RL6077-derived population, APR to stripe rust was also tightly linked with cfd71 on chromosome 4DL. An allele survey of linked SSR markers cfd71 and cfd23 on a set of 247 wheat lines from diverse origins indicated that these markers can be used to select for the donor segment in most wheat backgrounds. Comparison of RL6077 with Thatcher in field trials showed no effect of the APR gene on important agronomic or quality traits. Since no other known Lr genes exist on chromosome 4DL, the APR gene in RL6077 has been assigned the name Lr67.

QTL mapping for adult-plant resistance to stripe rust in Italian common wheat cultivars Libellula and Strampelli

Italian common wheat cultivars Libellula and Strampelli, grown for over three decades in Gansu province of China, have shown effective resistance to stripe rust. To elucidate the genetic basis of the resistance, F(3) populations were developed from crosses between the two cultivars and susceptible Chinese wheat cultivar Huixianhong. The F(3) lines were evaluated for disease severity in Beijing, Gansu and Sichuan from 2005 to 2008. Joint- and single-environment analyses by composite interval mapping identified five quantitative trait loci (QTLs) in Libellula for reduced stripe rust severity, designated QYr.caas-2DS, QYr.caas-4BL, QYr.caas-5BL.1, QYr.caas-5BL.2 and QYr.caas-7DS, and explained 8.1-12.4, 3.6-5.1, 3.4-8.6, 2.6 and 14.6-35.0%, respectively, of the phenotypic variance across four environments. Six interactions between different pairs of QTLs explained 3.2-7.1% of the phenotypic variance. The QTLs QYr.caas-4BL, QYr.caas-5BL.1 and QYr.caas-7DS were also detected in Strampelli, explaining 4.5, 2.9-5.5 and 17.1-39.1% of phenotypic variance, respectively, across five environments. Three interactions between different pairs of QTLs accounted for 6.1-35.0% of the phenotypic variance. The QTL QYr.caas-7DS flanked by markers csLV34 and Xgwm295 showed the largest effect for resistance to stripe rust. Sequence analyses confirmed that the lines with the QYr.caas-7DS allele for resistance carried the resistance allele of the Yr18/Lr34 gene. Our results indicated that the adult-plant resistance gene Yr18 and several minor genes confer effective durable resistance to stripe rust in Libellula and Strampelli.

QTL identification and microphenotype characterisation of the developmentally regulated yellow rust resistance in the UK wheat cultivar Guardian

Yellow rust (causal agent: Puccinia striiformis f.sp. tritici) resistance in the UK wheat cultivar Guardian is developmentally regulated, resistance increasing as the plant matures. Yellow rust resistance was assessed under field conditions on plants after ear emergence to ensure maximum expression of resistance. Three quantitative trait loci (QTL) for yellow rust resistance were identified, being located on chromosomes 1B (QPst.jic-1B), 2D (QPst.jic-2D) and 4B (QPst.jic-4B). The largest resistance effect, QPst.jic-1B located to the same position on the long arm of chromosome 1B as the known durable source of yellow rust resistance, Yr29. Microscopic studies were carried out to determine what effect the resistance in Guardian had on the development of P. striiformis f.sp. tritici. While the adult plant resistance in Guardian did not prevent germinated urediniospores from establishing an effective infection site, the growth of hyphae within flag leaf tissue was significantly inhibited, slowing the development of microcolonies. 3,3-diaminabenzadine (DAB) and trypan blue staining indicated that this inhibition of hyphal growth was not associated with hydrogen peroxide accumulation or extensive plant cell death.

The adult plant rust resistance loci Lr34/Yr18 and Lr46/Yr29 are important determinants of partial resistance to powdery mildew in bread wheat line Saar

Powdery mildew, caused by Blumeria graminis f. sp. tritici is a major disease of wheat (Triticum aestivum L.) that can be controlled by resistance breeding. The CIMMYT bread wheat line Saar is known for its good level of partial and race non-specific resistance, and the aim of this study was to map QTLs for resistance to powdery mildew in a population of 113 recombinant inbred lines from a cross between Saar and the susceptible line Avocet. The population was tested over 2 years in field trials at two locations in southeastern Norway and once in Beijing, China. SSR markers were screened for association with powdery mildew resistance in a bulked segregant analysis, and linkage maps were created based on selected SSR markers and supplemented with DArT genotyping. The most important QTLs for powdery mildew resistance derived from Saar were located on chromosomes 7DS and 1BL and corresponded to the adult plant rust resistance loci Lr34/Yr18 and Lr46/Yr29. A major QTL was also located on 4BL with resistance contributed by Avocet. Additional QTLs were detected at 3AS and 5AL in the Norwegian testing environments and at 5BS in Beijing. The population was also tested for leaf rust (caused by Puccinia triticina) and stripe rust (caused by P. striiformis f. sp. tritici) resistance and leaf tip necrosis in Mexico. QTLs for these traits were detected on 7DS and 1BL at the same positions as the QTLs for powdery mildew resistance, and confirmed the presence of Lr34/Yr18 and Lr46/Yr29 in Saar. The powdery mildew resistance gene at the Lr34/Yr18 locus has recently been named Pm38. The powdery mildew resistance gene at the Lr46/Yr29 locus is designated as Pm39.

Molecular mapping of genes for race-specific overall resistance to stripe rust in wheat cultivar Express

'Express', a hard red spring wheat cultivar that has been widely grown in the western United States, is used to differentiate races of Puccinia striiformis f. sp. tritici, the causal fungal pathogen of wheat stripe rust. To identify genes conferring race-specific, overall resistance to stripe rust, Express was crossed with 'Avocet S'. The parents and F(1), F(2), F(3) and F(5) populations were tested with races PST-1, PST-21, PST-43, and PST-45 of P. striiformis f. sp. tritici in the seedling stage under controlled greenhouse conditions. Two dominant genes for resistance to stripe rust were identified, one conferring resistance to PST-1 and PST-21, and the other conferring resistance to all four races. Linkage groups were constructed for the resistance genes using 146 F(5) lines to establish resistance gene analog and chromosome-specific simple sequence repeat marker polymorphisms. The gene for resistance to races PST-1 and PST-21 was mapped on the long arm of chromosome 1B, and that conferring resistance to all four races was mapped on the long arm of chromosome 5B. We temporarily designate the gene on 1BL as YrExp1 and the gene on 5BL as YrExp2. Polymorphism of at least one of the two markers flanking YrExp2 was detected in 91% of the 44 tested wheat genotypes, suggesting that they would be useful in marker-assisted selection for combining the gene with other resistance genes into many other wheat cultivars. Knowledge of these genes will be useful to understand recent virulence changes in the pathogen populations.

The adult plant rust resistance loci Lr34/Yr18 and Lr46/Yr29 are important determinants of partial resistance to powdery mildew in bread wheat line Saar

Powdery mildew, caused by Blumeria graminis f. sp. tritici is a major disease of wheat (Triticum aestivum L.) that can be controlled by resistance breeding. The CIMMYT bread wheat line Saar is known for its good level of partial and race non-specific resistance, and the aim of this study was to map QTLs for resistance to powdery mildew in a population of 113 recombinant inbred lines from a cross between Saar and the susceptible line Avocet. The population was tested over 2 years in field trials at two locations in southeastern Norway and once in Beijing, China. SSR markers were screened for association with powdery mildew resistance in a bulked segregant analysis, and linkage maps were created based on selected SSR markers and supplemented with DArT genotyping. The most important QTLs for powdery mildew resistance derived from Saar were located on chromosomes 7DS and 1BL and corresponded to the adult plant rust resistance loci Lr34/Yr18 and Lr46/Yr29. A major QTL was also located on 4BL with resistance contributed by Avocet. Additional QTLs were detected at 3AS and 5AL in the Norwegian testing environments and at 5BS in Beijing. The population was also tested for leaf rust (caused by Puccinia triticina) and stripe rust (caused by P. striiformis f. sp. tritici) resistance and leaf tip necrosis in Mexico. QTLs for these traits were detected on 7DS and 1BL at the same positions as the QTLs for powdery mildew resistance, and confirmed the presence of Lr34/Yr18 and Lr46/Yr29 in Saar. The powdery mildew resistance gene at the Lr34/Yr18 locus has recently been named Pm38. The powdery mildew resistance gene at the Lr46/Yr29 locus is designated as Pm39.

Identification and Molecular Characterization of Leaf Rust Resistance Gene Lr14a in Durum Wheat

Leaf rust, caused by Puccinia triticina, is an important disease of durum wheat (Triticum turgidum subsp. durum) and only a few designated resistance genes are known to occur in this crop. A dominant leaf rust resistance gene in the Chilean durum cv. Llareta INIA was mapped to chromosome arm 7BL through bulked segregant analysis using the amplified fragment length polymorphism (AFLP) technique, and by mapping three polymorphic markers in the common wheat (T. aestivum) International Triticeae Mapping Initiative population. Several simple sequence repeat (SSR) markers, including Xgwm344-7B and Xgwm146-7B, were associated with the leaf rust resistance gene. Resistance response and chromosomal position indicated that this gene is likely to be Lr14a. The SSR markers Xgwm344-7B and Xgwm146-7B and one AFLP marker also differentiated common wheat cv. Thatcher from the near-isogenic line with Lr14a, as well as durum 'Altar C84' from durum wheat with Lr14a. This is the first report of the presence of Lr14a in durum wheat, although the gene originally was transferred from emmer wheat 'Yaroslav' to common wheat. Lr14a is also present in CIMMYT-derived durum 'Somateria' and effective against Mexican and other P. triticina races of durum origin. Lr14a should be deployed in combination with other effective leaf rust resistance genes to prolong its effectiveness in durum wheat.

Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure

Linkage disequilibrium can be used for identifying associations between traits of interest and genetic markers. This study used mapped diversity array technology (DArT) markers to find associations with resistance to stem rust, leaf rust, yellow rust, and powdery mildew, plus grain yield in five historical wheat international multienvironment trials from the International Maize and Wheat Improvement Center (CIMMYT). Two linear mixed models were used to assess marker-trait associations incorporating information on population structure and covariance between relatives. An integrated map containing 813 DArT markers and 831 other markers was constructed. Several linkage disequilibrium clusters bearing multiple host plant resistance genes were found. Most of the associated markers were found in genomic regions where previous reports had found genes or quantitative trait loci (QTL) influencing the same traits, providing an independent validation of this approach. In addition, many new chromosome regions for disease resistance and grain yield were identified in the wheat genome. Phenotyping across up to 60 environments and years allowed modeling of genotype x environment interaction, thereby making possible the identification of markers contributing to both additive and additive x additive interaction effects of traits.

Inheritance of resistance to stripe rust in winter wheat cultivars Aquileja and Xian Nong 4

Winter wheat cultivars Aquileja (AQ) and Xian Nong 4(XN) were previously reported to possess durable, quantitative resistance to stripe rust disease. In the present study, AQ, XN and a susceptible wheat cultivar were reciprocally crossed in all 6 combinations. Parents, F1, F2, F3, BCP1 and BCP2 were used to determine quantitative genetic parameters for infection type and disease severity. The results showed that fixable genetic components preponderated in the inheritance of the resistance in AQ and XN for both infection type and disease severity, while the dominant component could be detected in some cases. The resistance was conditioned by oligogenes. Heritability of the resistance ranged from 50 to 79% in most cases.

Characterization of genetic loci conferring adult plant resistance to leaf rust and stripe rust in spring wheat

Leaf (brown) and stripe (yellow) rusts, caused by Puccinia triticina and Puccinia striiformis, respectively, are fungal diseases of wheat (Triticum aestivum) that cause significant yield losses annually in many wheat-growing regions of the world. The objectives of our study were to characterize genetic loci associated with resistance to leaf and stripe rusts using molecular markers in a population derived from a cross between the rust-susceptible cultivar 'Avocet S' and the resistant cultivar 'Pavon76'. Using bulked segregant analysis and partial linkage mapping with AFLPs, SSRs and RFLPs, we identified 6 independent loci that contributed to slow rusting or adult plant resistance (APR) to the 2 rust diseases. Using marker information available from existing linkage maps, we have identified additional markers associated with resistance to these 2 diseases and established several linkage groups in the 'Avocet S' x 'Pavon76' population. The putative loci identified on chromosomes 1BL, 4BL, and 6AL influenced resistance to both stripe and leaf rust. The loci on chromosomes 3BS and 6BL had significant effects only on stripe rust, whereas another locus, characterized by AFLP markers, had minor effects on leaf rust only. Data derived from Interval mapping indicated that the loci identified explained 53% of the total phenotypic variation (R2) for stripe rust and 57% for leaf rust averaged across 3 sets of field data. A single chromosome recombinant line population segregating for chromosome 1B was used to map Lr46/Yr29 as a single Mendelian locus. Characterization of slow-rusting genes for leaf and stripe rust in improved wheat germplasm would enable wheat breeders to combine these additional loci with known slow-rusting loci to generate wheat cultivars with higher levels of slow-rusting resistance.

Wheat rust resistance research at CSIRO

Although chemical control is available for rust diseases in wheat, economic and environmental factors favour genetic solutions. Maintenance and improvement of levels of resistance and durability of the genetic control of the 3 wheat rust diseases will occur with the application of DNA markers for pyramiding resistance genes. Information about the molecular basis of rust resistance, including durable, adult-plant resistance, coming from studies in model species such as flax and flax rust and from studies of wheat and barley, will provide knowledge for new biotechnological approaches to rust resistance. Increasing cereal gene sequence data will improve the efficiency of cloning disease resistance genes and, together with the rapid progress in understanding the molecular basis of rust resistance, will make it possible to construct transgenic plants with multiple rust resistance genes at a single locus, which will provide efficient breeding and increased durability of rust resistance.

Temporal gene expression profiling of the wheat leaf rust pathosystem using cDNA microarray reveals differences in compatible and incompatible defence pathways

In this study, we detail the construction of a custom cDNA spotted microarray containing 7728 wheat ESTs and the use of the array to identify host genes that are differentially expressed upon challenges with leaf rust fungal pathogens. Wheat cultivar RL6003 (Thatcher Lr1) was inoculated with Puccinia triticina virulence phenotypes BBB (incompatible) or TJB (7-2) (compatible) and sampled at four different time points (3, 6, 12, and 24 hours) after inoculation. Transcript expression levels relative to a mock treatment were measured. One hundred ninety two genes were found to have significantly altered expression between the compatible and incompatible reactions. Among those were genes involved in photosynthesis, the production of reactive oxygen species, ubiquitination, signal transduction, as well as in the shikimate/phenylpropanoid pathway. These data indicate that various metabolic pathways are affected, some of which might be used by RL6003 to mount a coordinated defense against an incompatible fungal pathogen.

High genetic diversity in Chilean populations of wheat yellow rust (Puccinia striiformis f. sp. tritici West.) assessed by RAPD and AFLP

Wheat yellow rust (Puccinia striiformis f. sp. tritici West. PST) is one of the main fungal diseases that causes major yield losses in the central and southern wheat production area of Chile. Chilean plant breeding programs have been using specific resistance genes to control this disease and resistance was frequently lost due to the appearance of new pathotypes of this pathogen. This resulted in a frequent change of wheat cultivars in the country. The objective of this work was to determine the genetic polymorphism among PST samples collected in wheat fields throughout the country, using randomly amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP). Twenty-nine PST populations from 5 locations were analysed with 64 RAPD primers and 6 combinations of AFLP primers. The coefficients of similarity (53% for RAPD and 14% for AFLP) indicated that the populations of yellow rust in Chile are highly diverse, in contrast with similar studies performed in other countries. This observation is supported by the virulence spectrum of PST population. This stressed the need to pyramid 2 or more major genes in commercial cultivars. Alternatively, the deployment of adult plant resistance gene combinations should be conducted. AFLP technique was more robust for analysis of the genetic diversity of PST compared with RAPD, because of its reproducibility and high level of polymorphism. The analysis of genetic similarity data among yellow rust populations grouped most of the PST population according to their geographic origin.

Resistance to cereal rusts at the plant cell wall—what can we learn from other host-pathogen systems?

The ability of plant cells to resist invasion by pathogenic fungi at the cell periphery (pre-invasion resistance) differs from other types of resistance that are generally triggered after parasite entry and during differentiation of specialised intracellular feeding structures. Genetic sources of pre-invasion resistance such as mlo for barley powdery mildew and Lr34 for resistance to wheat leaf rust have proven to be broad-spectrum in effect and durable in the field. Continued breeding for this type of resistance (often quantitative in effect) is therefore considered an important strategy to protect cereal crops long-term against potentially devastating fungal diseases such as rusts. Considerable progress has been made in characterising genes and processes underlying pre-invasion resistance using mutant analysis, molecular genetics, gene cloning, and the model plant Arabidopsis, as well as comparative functional analysis of genes in Arabidopsis and cereals. This review summarises the current knowledge in this field, and discusses several aspects of pre-invasion resistance potentially pertinent to use in breeding; namely, biological cost of the resistance and effectiveness of individual resistance genes against multiple pathogen types. We show that mutations in Mlo, Ror1, and Ror2 genes known to affect powdery mildew pre-invasion resistance have no detectable effect on partial resistance to barley leaf rust as measured by latency period.

Seedling and Slow Rusting Resistance to Stripe Rust in Chinese Common Wheats

Identification of seedling and slow stripe rust resistance genes is important for gene pyramiding, gene deployment, and developing slow-rusting wheat cultivars to control the disease. A total of 98 Chinese lines were inoculated with 26 pathotypes of Puccinia striiformis f. sp. tritici for postulation of stripe rust resistance genes effective at the seedling stage. A total of 135 wheat lines were planted at two locations to characterize their slow rusting responses to stripe rust in the 2003-2004 and 2004-2005 cropping seasons. Genes Yr2, Yr3a, Yr4a, Yr6, Yr7, Yr9, Yr26, Yr27, and YrSD, either singly or in combinations, were postulated in 72 lines, whereas known resistance genes were not identified in the other 26 accessions. The resistance genes Yr9 and Yr26 were found in 42 and 19 accessions, respectively. Yr3a and Yr4a were detected in two lines, and four lines may contain Yr6. Three lines were postulated to possess YrSD, one carried Yr27, and one may possess Yr7. Thirty-three lines showed slow stripe rusting resistance at two locations in both seasons.

Leaf tip necrosis, molecular markers and beta1-proteasome subunits associated with the slow rusting resistance genes Lr46/Yr29

Resistance based on slow-rusting genes has proven to be a useful strategy to develop wheat cultivars with durable resistance to rust diseases in wheat. However this type of resistance is often difficult to incorporate into a single genetic background due to the polygenic and additive nature of the genes involved. Therefore, markers, both molecular and phenotypic, are useful tools to facilitate the use of this type of resistance in wheat breeding programs. We have used field assays to score for both leaf and yellow rust in an Avocet-YrA x Attila population that segregates for several slow-rusting leaf and yellow rust resistance genes. This population was analyzed with the AFLP technique and the slow-rusting resistance locus Lr46/Yr29 was identified. A common set of AFLP and SSR markers linked to the Lr46/Yr29 locus was identified and validated in other recombinant inbred families developed from single chromosome recombinant populations that segregated for Lr46. These populations segregated for leaf tip necrosis (LTN) in the field, a trait that had previously been associated with Lr34/Yr18. We show that LTN is also pleiotropic or closely linked to the Lr46/Yr29 locus and suggest that a new Ltn gene designation should be given to this locus, in addition to the one that already exists for Lr34/Yr18. Coincidentally, members of a small gene family encoding beta-1 proteasome subunits located on group 1L and 7S chromosomes implicated in plant defense were linked to the Lr34/Yr18 and Lr46/Yr29 loci.

Targeted mapping of ESTs linked to the adult plant resistance gene Lr46 in wheat using synteny with rice

The gene Lr46 has provided slow-rusting resistance to leaf rust caused by Puccinia triticina in wheat (Triticum aestivum), which has remained durable for almost 30 years. Using linked markers and wheat deletion stocks, we located Lr46 in the deletion bin 1BL (0.84-0.89) comprising 5% of the 1BL arm. The distal part of chromosome 1BL of wheat is syntenic to chromosome 5L of rice. Wheat expressed sequence tags (ESTs) mapping in the terminal 15% of chromosome 1BL with significant homology to sequences from the terminal region of chromosome 5L of rice were chosen for sequence-tagged site (STS) primer design and were mapped physically and genetically. In addition, sequences from two rice bacterial artificial chromosome clones covering the targeted syntenic region were used to identify additional linked wheat ESTs. Fourteen new markers potentially linked to Lr46 were developed; eight were mapped in a segregating population. Markers flanking (2.2 cM proximal and 2.2 cM distal) and cosegregating with Lr46 were identified. The physical location of Lr46 was narrowed to a submicroscopic region between the breakpoints of deletion lines 1BL-13 [fraction length (FL)=0.89-1] and 1BL-10 (FL=0.89-3). We are now developing a high-resolution mapping population for the positional cloning of Lr46.

Identification, Chromosome Location, and Diagnostic Markers for a New Gene (YrCN19) for Resistance to Wheat Stripe Rust

ABSTRACT Several wheat lines and cultivars of wheat (Triticum aestivum) originating from the southwestern region of China were found to be highly resistant to stripe rust by inoculation with the prevalent races (CYR30, CYR31, and CYR32) and newly emerged races (H46-4, SY11-4 and SY11-14) of the pathogen. An inheritance study of the resistance to stripe rust was carried out by crossing resistant AIM6 with susceptible BeiZ76. Results indicated that the resistance to stripe rust was controlled by a single dominant gene. The 112 F(2) plants chosen from the cross BeiZ76/ AIM6 were analyzed with 218 pairs of microsatellite primers to determine the map location of the resistance gene. A simple sequence repeat marker on chromosome arm 2BS, Xgwm410, showed polymorphism and co-segregation between stripe rust resistant and susceptible plants. From the pedigree, inheritance, molecular marker, and resistance response, it is concluded that the stripe rust resistance gene in wheat cv. Chuan-nong19 (CN19) and wheat lines AIM5 and AIM6 is a novel gene, designated YrCN19. The microsatellite primer Xgwm410 is a diagnostic marker of the resistance gene YrCN19, which has potential for application in the marker-assisted breeding of wheat.

Molecular characterization of durum and common wheat recombinant lines carrying leaf rust resistance (Lr19) and yellow pigment (Y) genes from Lophopyrum ponticum

Chromosome 7E from Lophopyrum ponticum carries a valuable leaf rust resistant gene designated Lr19. This gene has not been widely used in common wheat breeding because of linkage with the yellow pigment gene Y. This gene tints flour yellow, reducing its appeal in bread making. However, a high level of yellow pigment is desirable in durum wheat breeding. We produced 97 recombinant chromosomes between L. ponticum transfer 7D.7E#1 and its wheat homoeologues, using the ph1b mutation that promotes homoeologous pairing. We characterized a subset of 37 of these lines with 11 molecular markers and evaluated their resistance to leaf rust and the abundance of yellow pigment. The Lr19 gene was mapped between loci Xwg420 and Xmwg2062, whereas Y was mapped distal to Xpsr687, the most distal marker on the long arm of chromosome 7. A short terminal 7EL segment translocated to 7A, including Lr19 and Y (line 1-23), has been transferred to durum wheat by backcrossing. The presence of this alien segment significantly increased the abundance of yellow pigment. The Lr19 also conferred resistance to a new durum leaf rust race from California and Mexico that is virulent on most durum wheat cultivars. The new durum lines with the recombinant 7E segment will be useful parents to increase yellow pigment and leaf rust resistance in durum wheat breeding programs. For the common wheat breeding programs, we selected the recombinant line 1-96, which has an interstitial 7E segment carrying Lr19 but not Y. This recombinant line can be used to improve leaf rust resistance without affecting flour color. The 7EL/7DL 1-96 recombinant chromosome did not show the meiotic self-elimination previously reported for a 7EL/7BL translocation.

Mapping of QTLs prolonging the latent period of Puccinia triticina infection in wheat

Slow rusting is considered a crucial component of durable resistance to wheat leaf rust caused by Puccinia triticina and is often expressed in the form of a prolonged latent period. Selection for a longer latent period is considered an effective approach to developing wheat cultivars with improved durable resistance to leaf rust. A recombinant inbred line (RIL) population derived from CI 13227 (long latent period) x Suwon 92 (short latent period) was phenotyped for latent period in two greenhouse experiments in separate years, and amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers were analyzed in the same population. Among the RILs, the frequency distribution for latent period was continuous, and latent period was highly correlated between years (r=0.94, P<0.0001). A quantitative trait locus (QTL) prolonging the latent period of P. triticina, designated as QLrlp.osu-2DS, explained 42.8% and 54.5% of the phenotypic and genetic variance in the two experiments, respectively. QLrlp.osu-2DS was mapped on the distal region of chromosome 2DS. Two other QTLs for latent period, QLrlp.osu-2B and QLrlp.osu-7BL, were localized on chromosome 2B and the long arm of chromosome 7B, respectively. Multiple regression analysis showed that these three QTLs collectively explained 58.0% and 73.8% of the phenotypic and genetic variance over two experiments, respectively. Fourteen RILs that carried all three alleles for long latent period at three AFLP loci flanking QLrlp.osu-2DS, QLrlp.osu-2B, and QLrlp.osu-7BL had a mean latent period of 12.5 days, whereas 13 RILs without any long-latent-period alleles at the corresponding loci had a mean latent period of 7.4 days. Three SSR markers closely linked to these QTLs have potential to be applied in marker-assisted selection for prolonged latent period in wheat.

A genetic analysis of adult plant resistance to stripe rust in the wheat cultivar Kariega

The wheat cultivar Kariega expresses complete adult plant resistance to stripe rust in South Africa. The aim of this investigation was to determine the extent and nature of variability in stripe rust resistance in a population of 150 doubled haploid lines generated from a cross between Kariega and the susceptible cultivar Avocet S. Analysis of field data for adult plant stripe rust resistance identified two major QTLs and two minor QTLs in the resistant cultivar Kariega. The two major QTLs were located on chromosomes 7D ( QYr.sgi-7D) and 2B ( QYr.sgi-2B.1), contributing 29% and 30% to the phenotypic variance, respectively. QYr.sgi-2B.1 is primarily associated with a chlorotic and/or necrotic response, unlike QYr.sgi-7D, which is believed to be the adult plant resistance gene Yr18. These two QTLs for adult plant resistance in Kariega appear to represent different forms of resistance, where QYr.sgi-7D may represent potentially more durable resistance than QYr.sgi-2B.1. Mixture model analysis of the field leaf infection scores suggested a genetic model involving two independent genes combining in a classical, epistatic manner. The results of the QTL analysis demonstrate its higher resolution power compared to the mixture model analysis by detecting the presence of minor QTLs.

Dissection of quantitative and durable leaf rust resistance in Swiss winter wheat reveals a major resistance QTL in the Lr34 chromosomal region

The Swiss winter bread wheat cv. 'Forno' has a highly effective, durable and quantitative leaf rust ( Puccinia triticina Eriks.) resistance which is associated with leaf tip necrosis (LTN). We studied 240 single seed descent lines of an 'ArinaxForno' F(5:7 )population to identify and map quantitative trait loci (QTLs) for leaf rust resistance and LTN. Percentage of infected leaf area (%) and the response to infection (RI) were evaluated in seven field trials and were transformed to the area under the disease progress curves (AUDPC). Using composite interval mapping and LOD >4.4, we identified eight chromosomal regions specifically associated with resistance. The largest and most consistent leaf rust resistance locus was identified on the short arm of chromosome 7D (32.6% of variance explained for AUDPC_% and 42.6% for AUDPC_RI) together with the major QTL for LTN ( R(2)=55.6%) in the same chromosomal region as Lr34 ( Xgwm295). A second major leaf rust resistance QTL ( R(2)=28% and 31.5%, respectively) was located on chromosome arm 1BS close to Xgwm604 and was not associated with LTN. Additional minor QTLs for LTN (2DL, 3DL, 4BS and 5AL) and leaf rust resistance were identified. These latter QTLs might correspond to the leaf rust resistance genes Lr2 or Lr22 (2DS) and Lr14a (7BL).